The Welsh Government delivered a snub to Education Secretary Michael Gove's English Baccalaureate last night, announcing that it intends to stick to GCSEs when the new exam is introduced in two years' time.
The move signals an end to the common examination system between the countries which has existed since the birth of state education.
The two countries may also diverge on A-levels, with the Welsh Deputy Skills Minister, Jeff Cuthbert, saying Mr Gove's plan to reform that exam "has little appeal".
Welsh headteachers backed the minister, with Gareth Jones, general secretary of ASCL Cymru, saying: "It makes huge sense to keep the same qualification for all students rather than moving to a two-tier system of education. [The Welsh Assembly] has made the decision that's right for the children of Wales."
Announcing the move last night, Mr Cuthbert said the Welsh Assembly intended to stick with GCSEs and A-levels after an independent study found the examinations had a proven international track record.
Mr Gove intends to replace GCSEs in the core academic subjects of maths, English, the sciences, languages, history and geography with EBacc certificates in 2015. He also plans to make A-levels more rigorous.
The spotlight now turns on Northern Ireland, which also uses the same exams system as England but where headteachers are concerned about adopting EBaccs in some subjects and GCSEs in others. A review of the system reports in June.